Labeling with heavy atom clusters attached to antibody fragments is an attractive technique for determining the 3D distribution of specific proteins in cells using electron tomography in the electron microscope. However, the small size of the labels makes them very difficult to detect by conventional bright-field electron tomography. We have developed a technique based on quantitative scanning transmission electron microscopy (STEM) by making use of a large-angle annular dark-field detector and a small-angle axial bright-field detector. Using the dark-field technique, we have demonstrated that it is possible to detect 11-gold atom clusters and Nanogold clusters containing approximately 67 gold atoms in cells that are sectioned to a thickness of around 100 nm. STEM tomography has the potential to localize specific proteins in permeabilized cells using antibody fragments tagged with small heavy atom clusters. Our quantitative analysis provides a framework for determining the detection limits and optimal experimental conditions for localizing these small clusters. We have also investigated the application of STEM tomography to image thicker sections of eukaryotic cells. Conventional bright-field electron tomographic tilt series are obtained by collecting electrons that have traversed a specimen illuminated by a broad beam. Using this approach, the thickness is limited by the severe image blurring that occurs when electrons that have undergone multiple energy losses are focused by the objective lens of the microscope. Furthermore, the maximum area of the image is limited by the depth-of-field of the objective lens, so that only part of the sample is in focus at high tilt angles. Tomographic reconstruction using STEM with a tightly focused electron probe can overcome some of the limitations imposed by tomographic reconstruction using conventional TEM. First, because the incident STEM probe can be focused at any point in a specimen, large areas are imaged in focus even for high tilt angles. Second, because in STEM there are no image-forming lenses after the specimen, the resolution attainable in images of thick specimens is not further degraded by electrons that have suffered multiple energy losses. The most commonly applied STEM approach makes use of an annular dark-field detector to collect electrons that are scattered to high angles. However, the drak-field STEM technique is not well-suited to imaging thick biological specimens because of the limited depth of field defined by the large convergence angle of the incident electron probe. A tenfold or higher increase in depth of field is possible by adjusting the microscope optics to decrease the convergence semi-angle to approximately 12 mrad. Another limiting feature of dark-field STEM as applied to imaging thick specimens is the severe degradation in spatial resolution that occurs toward the bottom surface of a section because of beam broadening. In contrast, we found that much higher spatial resolution can be obtained by collecting only those electrons that are scattered to low angles, that is, by using an axial bright-field detector. Electrons that undergo multiple elastic scattering are substantially displaced from the point of incidence of the STEM probe and have, on average, larger net scattering angles. A large fraction of these electrons can thus be excluded from images recorded with an axial detector, leading to an improvement in spatial resolution toward the bottom surface of thick specimens. We quantified this unexpected improvement in resolution using Monte Carlo electron-trajectory simulations. Tomogram slices of infected erythrocytes revealed parasites during the process of schizogany. The dynamics of organellogenesis and morphogenesis in Plasmodium falciparum are poorly understood because of the laborious procedure of conventional 3D reconstructions from serial thin sections. Using STEM-based tomography with an axial detector, however, enables more rapid reconstruction of entire schizonts, which allows a series of cells to be studied and the sequence of morphological events to be established. The 3D model derived from the tomograms revealed the spatial arrangements of several major organelles, including nuclei, rhoptries, food vacuole, Golgi complex, apicoplast and lipid body. Stacks of what we believe to be hitherto unreported endoplasmic reticulum were also observed. In addition to these organelles, three layers of membranes surrounding the schizont were clearly identifiable: parasite plasma membrane, the parasitophorus vacuole membrane, and the erythrocyte membrane. Other parasite-derived membrane structures (for example, tubular extensions of the vacuolar membrane, Maurers clefts and circular clefts) were also visible inside erythrocyte cytoplasm. Thus, a new ultrastructural method is now available to study the complex dynamics of malaria parasite development inside human erythrocytes. Thus we have demonstrated the feasibility and advantages of STEM using axial detection for imaging thick sections at a spatial resolution around 510 nm, which is comparable to the spatial resolution of conventional electron tomography from thinner sections (typically 38 nm). Most modern electron microscopes can be operated in STEM mode and can be readily equipped with a bright-field detector, which is anticipated to facilitate implementation of the technique. The demand for high-resolution, large-volume imaging of biological specimens has been addressed so far by the large-scale application of conventional electron tomography of thin sections. Our current work suggests that it will be possible to reconstruct intact organelles, intracellular pathogens and even entire mammalian cells through serial thick-section tomography. Axial STEM-based tomography could also be useful for the 3D characterization of multiphase polymers, biomaterials and other soft materials.